Instructions to run Trajectum at Nikhef
NOTE: This page is still work in progress!
Before you start running your jobs at Nikhef, please make sure you join the stbc-mattermost channel using the following link.
Pre-installed packages
The packages needed to configure trajectum are stored at: /project/alice/trajectum_packages
In this directory you find:
LHAPDF-6.5.4
fastjet-3.4.2gemini_2024.8.8pythia8309smashautoconf-archive
All users read and execute.
Access to Trajectum source code
In order to work on Trajectum you need to be part of the trajectum repository at codeberg.org
If you want you can request acces by creating an account, with your usename including: FirstnameLastname
Then send an email to ... including your username to get access.
Setting up Trajectum
The following steps can be used alongside the description of setting up Trajectum in the README file of the source code.
Set up the environment in bash with the following function:
setup_trajectum() {
source /cvmfs/alice.cern.ch/etc/login.sh
source /cvmfs/sft.cern.ch/lcg/views/setupViews.sh LCG_107 x86_64-el9-gcc14-opt
export PKG_CONFIG=/usr/bin/pkg-config
export LD_LIBRARY_PATH=/project/alice/trajectum_packages/pythia8309/lib/:/project/alice/trajectum_packages/lib/:$LD_LIBRARY_PATH
export GINPUT=/project/alice/trajectum_packages/share/gemini/
}
Alternatively, one can execute the commands inside the function.
Go to /data/alice/<yourNikhefusername> (or any other preferred directory)
Clone the Trajectum source code:
git clone https://codeberg.org/Trajectum/Trajectum.git
This will create a Trajectum directory. In this directory execute:
autoreconf --install -I /project/alice/trajectum_packages/autoconf-archive/m4/
which will create the configure executable with which you can run
./configure --with-lhapdf-prefix=/project/alice/trajectum_packages --with-fastjet-prefix=/project/alice/trajectum_packages --with-pythia-prefix=/project/alice/trajectum_packages/pythia8309 --with-gemini-prefix=/project/alice/trajectum_packages
Then execute (still in the Trajectum directory)
make
Executing collide
In order to run collide you need to set: (no need to do this if you set up your environment with setup_trajectum)
export LD_LIBRARY_PATH=/project/alice/trajectum_packages/pythia8309/lib/:/project/alice/trajectum_packages/lib/:$LD_LIBRARY_PATH export GINPUT=/project/alice/trajectum_packages/share/gemini/
Within the Trajectum directory change to src/
In the src directory execute
./collide ../parfiles/collisionpp.par
collisionpp.par is an example file with parameter setting for a pp collision. You can use all the example parameter files in parfiles/
This command should output 5 files starting with pp.
Compiling smash (next section more detailed)
To compile smash one first needs to setup the environment by selecting the proper gcc and rivet versions (note that everything i.e. pythia, collisions, needs to be compiled again):
source /cvmfs/alice.cern.ch/etc/login.sh source /cvmfs/sft.cern.ch/lcg/views/setupViews.sh LCG_104 x86_64-el9-gcc12-opt source /cvmfs/sft.cern.ch/lcg/releases/MCGenerators/rivet/3.1.8-79cbb/x86_64-el9-gcc12-opt/rivetenv.sh export PKG_CONFIG=/usr/bin/pkg-config export LD_LIBRARY_PATH=/data/alice/pchrist/Hydro/pythia8309/lib/:/project/alice/trajectum_packages/lib/:$LD_LIBRARY_PATH export GINPUT=/project/alice/trajectum_packages/share/gemini/ unset CMAKE_PREFIX_PATH export CMAKE_PREFIX_PATH=/data/alice/pchrist/Hydro/pythia8309
You then have to configure and compile pythia:
cd pythia8309 ./configure make
Go to the directory where smash is cloned, create the build directory and go inside:
cd smash mkdir build cd build
Then make and install:
cmake -DPythia_CONFIG_EXECUTABLE=/data/alice/pchrist/Hydro/pythia8309/bin/pythia8-config -DPYTHIA8_DIR=/data/alice/pchrist/Hydro/pythia8309 -DTRY_USE_ROOT=OFF -DBUILD_TESTING=OFF -DCMAKE_CXX_STANDARD=17 -DCMAKE_INSTALL_PREFIX=/data/alice/pchrist/Hydro/smash -S ../ -B /data/alice/pchrist/Hydro/Trajectum/smash/build
make install
Executing smash
I first used setup_trajectum to setup the environment.
First, inside your own directory in /data/alice, run:
mkdir smash git clone https://github.com/smash-transport/smash.git cd smash git checkout SMASH-3.0 mkdir build cd build
Now you are in the build directory inside the smash directory of your own directory.
We need to copy 5 header files that have been modified, from Panos' directory into your own, as such:
cp CMakeLists.txt /data/alice/<yourname>/smash cp src/include/smash/particletype.h /data/alice/<yourname>/smash/src/include/smash cp src/include/smash/pdgcode.h /data/alice/<yourname>/smash/src/include/smash cp src/include/smash/pdgcode_constants.h /data/alice/<yourname>/smash/src/include/smash cp src/include/smash/stringfunctions.h /data/alice/<yourname>/smash/src/include/smash
You can check if this worked by running git status which should output a list of the 5 header files that were modified. We are still in the smash/build directory.
We can now run cmake:
cmake -DPythia_CONFIG_EXECUTABLE=/data/alice/pchrist/Hydro/pythia8309/bin/pythia8-config -DPYTHIA8_DIR=/data/alice/pchrist/Hydro/pythia8309 -DTRY_USE_ROOT=OFF -DBUILD_TESTING=OFF -DCMAKE_CXX_STANDARD=17 -DCMAKE_INSTALL_PREFIX=/data/Alice/<yourname>/smash -S /data/Alice/<yourname>/smash -B /data/alice/<yourname>/smash/build
Then run
make install
No more error! (I hope)
Then we can use the output of the collide executable, which should be a set of 5 files: pp.main, pp.bypass, pp.extra, pp.geometry, and pp.input by first
cd /data/alice/<yourname>/trajectum/src
Note: make sure the output file, specifically pp.main, are located in that directory
Then rename pp.main and run smash
mv pp.main filename0 /data/alice/<yourname>/smash/build/smash -i /data/alice/<yourname>/Trajectum/parfiles/smash.yaml
This should feed smash with the right particle list file (filename0)
Note: make sure that the environment is set up, as indicated above (in the setup_trajectum function).
Known issues
If you already (before following the steps above) executed make in your Trajectum directory within a slightly different environment as setup in "Setting up Trajectum".
./collide ../parfiles/collisionpp.par can crash with a segmentation fault giving multiple errors containing: ./collide: Symbol `<name>' has different size in shared object, consider re-linking
If you get these errors, before executing make , execute make clean before following the rest of the remaining steps.
Run your Trajectum jobs on the Stoomboot cluster
For general information about the CPU Batch system at Nikhef and general guidelines on how to submit jobs, visit CT wiki and the HTCondor manual.
To submit your jobs to the Nikhef cluster you need a submission script <filename>.sub and an executable <filename>.sh that contains the code you want to execute.
An example submission script:
executable = testJob.sh log = test.log output = outfile.txt error = errors.txt +UseOS = "el9" +JobCategory = "short" request_cpus = 4 request_memory = 8G max_idle = 50 queue
If you need to pass arguments to your executable you can add them by adding the following line to your submission script:
arguments = "var1 var2 var3"
The workflow in your testJob.sh could contain the following
#!/bin/bash
source /cvmfs/alice.cern.ch/etc/login.sh
source /cvmfs/sft.cern.ch/lcg/views/setupViews.sh LCG_107 x86_64-el9-gcc14-opt
outdir=/path/to/directory/where/you/want/to/store/your/output/files
export TRAJECTUM_DIR=/path/to/Trajectum/directory
export PKG_CONFIG=/usr/bin/pkg-config
export LD_LIBRARY_PATH=/project/alice/trajectum_packages/pythia8309/lib/:/project/alice/trajectum_packages/lib/:$LD_LIBRARY_PATH
export GINPUT=/project/alice/trajectum_packages/share/gemini
#create output directory if it does not exist yet
if [! -d ${outdir} ]
then
mkdir -p ${outdir}
fi
cd ${TMPDIR}
pwd
${TRAJECTUM_DIR}/src/collide ${TRAJECTUM_DIR}/parfiles/collisionpp.par
ls
mv pp.* ${outdir}
echo "Anything left?"
ls
Make sure you point outdir and TRAJECTUM_DIR to the right directories.
Before submitting the submission file make sure that you make your shell script an executable by running chmod +x testJob.sh otherwise the system considers it to be just a text file and it will not run. If you submit the script like this, the log, output and error files will be created in the same directory as the submission file, add a different path if you'd like to save it elsewhere. Make sure you’ve completed all the steps on this wiki up to and including the “Executing Collide” section — specifically, up to successfully running make in your cloned Trajectum directory.
To submit your workflow run:
condor_submit <filename>.sub
You can check the status of your job using condor_q for more advanced commands please check the HTCondor manual.
And check your output, error & log files to see if everything works.
TIP: First test your executable on the interactive nodes to debug any issues, if it runs without problems submit it to the cluster!